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- PDB-5myx: Structure of Pyroglutamate-Abeta-specific Fab c#24 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5myx
TitleStructure of Pyroglutamate-Abeta-specific Fab c#24 in complex with human Abeta-pE3-18
Components
  • Fab c#24 heavy chain
  • Fab c#24 light chain
  • Pyroglutamate-Abeta pE3-18
KeywordsIMMUNE SYSTEM / Alzheimer's disease / pyroglutamate Abeta / monoclonal antibody / fibrillation
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / main axon / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / dendritic shaft / TAK1-dependent IKK and NF-kappa-B activation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / cellular response to amyloid-beta / neuron projection development / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of gene expression / regulation of translation / early endosome membrane / G alpha (i) signalling events / perikaryon / G alpha (q) signalling events / dendritic spine
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.492 Å
AuthorsParthier, C. / Piechotta, A. / Stubbs, M.T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and functional analyses of pyroglutamate-amyloid-beta-specific antibodies as a basis for Alzheimer immunotherapy.
Authors: Piechotta, A. / Parthier, C. / Kleinschmidt, M. / Gnoth, K. / Pillot, T. / Lues, I. / Demuth, H.U. / Schilling, S. / Rahfeld, J.U. / Stubbs, M.T.
History
DepositionJan 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 11, 2020Group: Atomic model / Data collection / Polymer sequence / Category: atom_site / entity_poly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab c#24 light chain
B: Fab c#24 heavy chain
C: Fab c#24 light chain
D: Fab c#24 heavy chain
E: Pyroglutamate-Abeta pE3-18
F: Pyroglutamate-Abeta pE3-18


Theoretical massNumber of molelcules
Total (without water)105,3306
Polymers105,3306
Non-polymers00
Water26,3381462
1
A: Fab c#24 light chain
B: Fab c#24 heavy chain
E: Pyroglutamate-Abeta pE3-18


Theoretical massNumber of molelcules
Total (without water)52,6653
Polymers52,6653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-30 kcal/mol
Surface area20040 Å2
MethodPISA
2
C: Fab c#24 light chain
D: Fab c#24 heavy chain
F: Pyroglutamate-Abeta pE3-18


Theoretical massNumber of molelcules
Total (without water)52,6653
Polymers52,6653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-25 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.611, 95.935, 90.371
Angle α, β, γ (deg.)90.000, 101.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-525-

HOH

21B-554-

HOH

31C-470-

HOH

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Components

#1: Antibody Fab c#24 light chain


Mass: 24134.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab c#24 heavy chain


Mass: 26562.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Pyroglutamate residue 1 (PCA) results from post-translational modification of original residue glutamine 1.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide Pyroglutamate-Abeta pE3-18


Mass: 1968.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1462 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% w/v PEG 3000 100 mM sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.49→47.967 Å / Num. obs: 154382 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.191 % / Biso Wilson estimate: 14.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Χ2: 0.989 / Net I/σ(I): 18.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.49-1.584.0550.6442.17228040.7180.74390
1.58-1.694.170.3973.61237580.870.45699.9
1.69-1.834.1940.2226.39221860.9540.25499.9
1.83-24.2170.11412.08203740.9880.13199.8
2-2.244.2410.06620.25184410.9960.07599.9
2.24-2.584.2520.04627.96163310.9980.05399.9
2.58-3.164.2430.0341137650.9990.03599.8
3.16-4.464.2290.0258.17107200.9990.02399.8
4.46-47.9674.1810.01664.03600310.01999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.97 Å
Translation2.5 Å47.97 Å

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Processing

Software
NameVersionClassification
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZEA

1zea


Resolution: 1.492→47.967 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.29
RfactorNum. reflection% reflection
Rfree0.2129 7719 5 %
Rwork0.1805 --
obs0.1821 154378 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.56 Å2 / Biso mean: 21.3039 Å2 / Biso min: 5.9 Å2
Refinement stepCycle: final / Resolution: 1.492→47.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6845 0 0 1462 8307
Biso mean---31.5 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057227
X-RAY DIFFRACTIONf_angle_d0.8329887
X-RAY DIFFRACTIONf_chiral_restr0.0811106
X-RAY DIFFRACTIONf_plane_restr0.0051271
X-RAY DIFFRACTIONf_dihedral_angle_d14.2262632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4915-1.50850.27391370.26832588272552
1.5085-1.52620.30962610.260249625223100
1.5262-1.54480.27342600.246649355195100
1.5448-1.56440.25142610.238449695230100
1.5644-1.5850.25842600.227149405200100
1.585-1.60670.26282610.229749625223100
1.6067-1.62960.24812600.224449385198100
1.6296-1.6540.26692610.217849625223100
1.654-1.67980.26162600.215149435203100
1.6798-1.70740.25482610.209849535214100
1.7074-1.73680.24352610.201749625223100
1.7368-1.76840.21812610.203149515212100
1.7684-1.80240.2432610.193749595220100
1.8024-1.83920.21292620.190649895251100
1.8392-1.87920.24122620.19149735235100
1.8792-1.92290.23722600.188349395199100
1.9229-1.9710.24332620.188849715233100
1.971-2.02430.21192600.181949405200100
2.0243-2.08380.21442610.183349575218100
2.0838-2.15110.21912610.181649745235100
2.1511-2.2280.24072610.17849495210100
2.228-2.31720.21282630.182449965259100
2.3172-2.42260.21862610.176249565217100
2.4226-2.55040.21922600.176249475207100
2.5504-2.71010.20862620.180949815243100
2.7101-2.91940.20482630.177649855248100
2.9194-3.21310.20442630.174150025265100
3.2131-3.67790.19032620.163549765238100
3.6779-4.63310.1652640.144850225286100
4.6331-47.99230.18412670.16350785345100

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